biomedical-informatics

Python wraper for MetaMap

Ontology for consent codes and data use requirements

Few- and Zero-shot Multi-Label Learning for Structured Label Spaces

MetaSRA: normalized sample-specific metadata for the Sequence Read Archive

Computational Analysis of Novel Drug Opportunities

Few- and Zero-shot Multi-Label Learning for Structured Label Spaces

Build project for all CEDAR Java repositories

ETUDE (Evaluation Tool for Unstructured Data and Extractions) is a Python-based tool that provides consistent evaluation options across a range of annotation schemata and corpus formats

BioMedICUS: A biomedical and clinical NLP engine.

CREAM (Clustering of Functional Regions Analysis Method) is a new method for identification of clusters of functional regions (COREs) within chromosomes.

R package for delineating temporal dataset shifts in Eletronic Health Records

Emory BMI GSoC 2020 Project Ideas

📎 About MIDA Project

Core components and documentation of the tranSMART platform.

Website for the JuliaHealth organization (powered by Franklin.jl).

An exploratory, tutorial and analytical view of the Unified Medical Language System (UMLS) & the software/technologies provided via being a free UMLS license holder. This repo will subset 2021AB UMLS native release, introduce/build upon UMLS provided tools to load a configured subset into first a relational database --> MySQL, SQLite, PostgreSQL and MariaDB all covered within this repo. Next the UMLS subset which is stored in a relational DB will be queried, modeled and lastly loaded into a defined Neo4j label property graph. Lastly, Neo4j database containing UMLS 2021AB subset in schema promoting intuitive analysis and rich visualization will become the central datastore for analysis. The datastore contains ~5 million distinct nodes & >40 million distinct relationships (edges). Currently, Neo4j is running via Docker but deployment options are NOT limited to Docker. If choosing to deploy via Neo4j Aura, server, Neo4j Desktop, VM etc... Please note and be aware of the specific volumes and environment variables specified within this repository (docker run). The ability for the loaded Neo4j Graph to interact with RDF data (i.e. import/export RDF data to and from Neo4j) may not be possible via all Neo4j deployment avenues (i.e. Neo4j Aura currently does not support RDF integration that is demonstrated in this repository).

A digital repository for biomedical data based on a flexible JSON data model ( The project has been moved to a new address https://github.com/xtens-suite/xtens-app.git )

R code for the discovery of COVID-19 subgroups by symptoms and comorbidities.

Measuring and visualizing biomedical data variability/heterogeneity across data sources

R package for translating between drug identifiers using the Chemical Translation Service (CTS)

Materials used for introductory classes using Julia for statistics, biomedical queries and plotting

Implementation of our matching network CNN

Perl implementation of Markov Chain for the course BIO331

Data ingest pipeline for OMIM.

The Github page of the Innovation Center for Biomedical Informatics (ICBI) at Georgetown University

Implementation of our matching network CNN

A PyTorch Wrapper of Hierarchical Attention Network with Sentence Objectives Framework for ARDS Identification

📝 Source code for my website, portfolio of projects, and more